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Re: [h5md-user] Variable-size particle groups

From: Peter Colberg
Subject: Re: [h5md-user] Variable-size particle groups
Date: Tue, 29 May 2012 06:48:49 -0400
User-agent: Mutt/1.5.21 (2010-09-15)

On Tue, May 29, 2012 at 11:38:22AM +0200, Olaf Lenz wrote:
> I just remembered another issue that comes up with varying particle
> numbers in a simulation: the particle identity. When a particle
> disappears from the simulation, are all other particle data afterwards
> shifted one down? In particular for visualization, this information is
> crucial.
> Therefore, in a simulation with varying particle number, it is probably
> necessary to add some way to identify a particle in the array, e.g. by
> adding another subgroup "particle_id[variable x N]" to the trajectory
> group.

Yes, then we should also specify a “particle_id” subgroup in H5MD
along with the optional “range” dataset for the subgroups.

> In general, standardizing such a subgroup might also be useful in
> simulations with fixed particle numbers, e.g. for parallel IO, where the
> particles are not always stored on the same CPU.

Am I correct that one would *always* want to write the particle
identities with parallel IO? Since particles move between processors,
a fixed order (e.g. the initial order) would require each processor to
perform a scattered write to the “value” dataset, which is probably
quite slow with HDF5. By storing particles according to their current
order in memory, each processor could write to a linear region in
the dataset.


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